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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "GALAHAD" in publications use:'
type: software
license: MIT
title: 'GALAHAD: Geometry-Adaptive Lyapunov-Assured Hybrid Optimizer with Softplus
  Reparameterization and Trust-Region Control'
version: 2.0.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.GALAHAD
abstract: Implements the GALAHAD algorithm (Geometry-Adaptive Lyapunov-Assured Hybrid
  Optimizer), updated in version 2 to replace the hard-clamp positivity constraint
  of v1 with a numerically smooth softplus reparameterization, add rho-based trust-region
  adaptation (actual vs. predicted objective reduction), extend convergence detection
  to include both absolute and relative function-stall criteria, and enrich the per-iteration
  history with Armijo backtrack counts and trust-region quality ratios. Parameters
  constrained to be positive (rates, concentrations, scale parameters) are handled
  in a transformed z-space via the softplus map so that gradients remain well-defined
  at the constraint boundary. A two-partition API (positive / euclidean) replaces
  the three-way T/P/E partition of v1; the legacy form is still accepted for backwards
  compatibility. Designed for biological modeling problems (germination, dose-response,
  prion RT-QuIC, survival) where rates, concentrations, and unconstrained coefficients
  coexist. Developed at the Minnesota Center for Prion Research and Outreach (MNPRO),
  University of Minnesota. Based on Conn et al. (2000) <https://doi.org/10.1137/1.9780898719857>,
  Barzilai and Borwein (1988) <https://doi.org/10.1093/imanum/8.1.141>, Xu and An
  (2024) <https://doi.org/10.48550/arXiv.2409.14383>, Polyak (1969) <https://doi.org/10.1016/0041-5553(69)90035-4>,
  Nocedal and Wright (2006, ISBN:978-0-387-30303-1), and Dugas et al. (2009) <https://www.jmlr.org/papers/v10/dugas09a.html>.
authors:
- family-names: Feiss
  given-names: Richard A.
  email: feiss026@umn.edu
  orcid: https://orcid.org/0009-0008-0409-6042
preferred-citation:
  type: manual
  title: 'GALAHAD: Geometry-Adaptive Lyapunov-Assured Hybrid Optimizer with Softplus
    Reparameterization and Trust-Region Control'
  authors:
  - family-names: Feiss
    given-names: Richard A.
    orcid: https://orcid.org/0009-0008-0409-6042
    email: feiss026@umn.edu
  year: '2026'
  notes: R package version 2.0.0
  url: https://CRAN.R-project.org/package=GALAHAD
repository: https://rfeissiv.r-universe.dev
repository-code: https://github.com/RFeissIV/GALAHAD
commit: d4dae00576659e07f0bf7e76fe7d98c52d190b27
url: https://github.com/RFeissIV/GALAHAD
date-released: '2026-03-08'
contact:
- family-names: Feiss
  given-names: Richard A.
  email: feiss026@umn.edu
  orcid: https://orcid.org/0009-0008-0409-6042